| Texto completo | |
| Autor(es): |
Cajahuaringa, Samuel
;
Zanotto, Leandro N.
;
Caetano, Daniel L. Z.
;
Rigo, Sandro
;
Yviquel, Herve
;
Skaf, Munir S.
;
Araujo, Guido
;
IEEE Comp Soc
Número total de Autores: 8
|
| Tipo de documento: | Artigo Científico |
| Fonte: | 2022 IEEE 34TH INTERNATIONAL SYMPOSIUM ON COMPUTER ARCHITECTURE AND HIGH PERFORMANCE COMPUTING (SBAC-PAD 2022); v. N/A, p. 10-pg., 2022-01-01. |
| Resumo | |
Ion Mobility coupled to Mass Spectrometry (IM-MS) has become a highly valued tool for structural characterization of biological samples. In IM-MS the protein under investigation is ionized and accelerated by an electric field into a drift tube where it collides against a buffer gas. The separation of the gas-phase ions is then measured through the differences in their rotationally averaged Collision Cross-Section (CCS) values. The utility of the measured CCS for structural characterization critically depends on the validation against its theoretical calculation, which relies on intensive molecular mechanics simulation. Increasing the performance of CCS simulation is thus a relevant computational-chemistry research problem. This work shows that the combination of a linked-cell based algorithm with parallelization techniques can considerably increase the performance of CCS simulation. Experimental results reveal speedups from similar to 10x up to similar to 400x and parallelization efficiency greater than 0.98 when compared to High Performance Collision Cross Section (HPCCS), an optimized solution for CCS simulation. This reduces the CCS computation time from hours to minutes for a large range of proteins, making the proposed method the most performant approach to this problem nowadays, to the best of our knowledge. (AU) | |
| Processo FAPESP: | 12/24750-6 - Relações entre a obesidade e o receptor TLR4: Novos estudos através de simulações de dinâmica molecular |
| Beneficiário: | Paulo Cesar Telles de Souza |
| Modalidade de apoio: | Bolsas no Brasil - Pós-Doutorado |
| Processo FAPESP: | 16/04963-6 - Dinâmica molecular de hidrólise enzimática de celulose e simulações de QM/MM de reações químicas em sistemas biomoleculares |
| Beneficiário: | Gabriel Heerdt |
| Modalidade de apoio: | Bolsas no Brasil - Pós-Doutorado |
| Processo FAPESP: | 13/08293-7 - CECC - Centro de Engenharia e Ciências Computacionais |
| Beneficiário: | Munir Salomao Skaf |
| Modalidade de apoio: | Auxílio à Pesquisa - Centros de Pesquisa, Inovação e Difusão - CEPIDs |
| Processo FAPESP: | 21/03224-3 - Computação de alto desempenho e dinâmica molecular |
| Beneficiário: | Oscar Samuel Cajahuaringa Macollunco |
| Modalidade de apoio: | Bolsas no Brasil - Pós-Doutorado |
| Processo FAPESP: | 19/19662-0 - Arquitetura mesoscópica de fibras lignocelulósicas |
| Beneficiário: | Daniel Lucas Zago Caetano |
| Modalidade de apoio: | Bolsas no Brasil - Pós-Doutorado |